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#' Function that loads forcings data for Mussel spatialized model and performs the interpolation
#'
#' @param userpath the path where folder containing model inputs and outputs is located
#' @return a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
#' @export
#'
#' @import matrixStats plotrix rstudioapi
#'
#' @import stats utils
#'
Mussel_spatial_dataloader<-function(userpath) {
# Reads point forcing files
POCtem=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Point forcings//POC.csv"),sep=",",header=FALSE) # Reading the POC (daily series) data
POCchtem=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Point forcings//POC_characterization.csv"),sep=",",header=FALSE) # Reading the POC composition data
POMtem=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Point forcings//POM.csv"),sep=",",header=FALSE) # Reading the individual POM time series (daily series) data
TSMtem=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Point forcings//TSM.csv"),sep=",",header=FALSE) # Reading the TSM (daily series) data
Spatial_dates=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//Spatial_dates.csv"),sep=",",header=FALSE)
# Reads integration extremes
Param_matrix=read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Parameters//Parameters.csv"),sep=",") # Reading the matrix containing parameters and their description
#Extracts vectors from the forcing files
Dates=Param_matrix[37:38,3] # Vector containing the starting and ending date of teh simulation
# Initial times for spatial forcings
timeT=as.matrix(Spatial_dates[2,2:3]) # Vector of the times of Temperature measurements
timeChla=as.matrix(Spatial_dates[3,2:3]) #Vector of the times of Chlorophyll a measurements
# Initial time for time series
timePOC=as.matrix(POCtem[,1]) # Vector of the times of POC measurements
POC=as.double(as.matrix(POCtem[,2])) # Vector of POC time series (daily series)
timePOCch=as.matrix(POCchtem[,1]) # Vector of POC characterization (C:N:P) time series (daily series)
CPOC=as.double(as.matrix(POCchtem[,2])) # Vector containing the C/P ratio of seston (weight ratio)
NPOC=as.double(as.matrix(POCchtem[,3])) # Vector containing the N/P ratio of seston (weight ratio)
timePOM=as.matrix(POMtem[,1]) # Vector of the times of POC measurements
POM=as.double(as.matrix(POMtem[,2])) # Vector of POC time series (daily series)
timeTSS=as.matrix(TSMtem[,1]) # Vector of the times of POC measurements
TSS=as.double(as.matrix(TSMtem[,2])) # Vector of POC time series (daily series)
# Times needed to perform interpolation
t0=min(as.numeric(as.Date(timeT[1], "%d/%m/%Y")), as.numeric(as.Date(timeChla[1], "%d/%m/%Y")), as.numeric(as.Date(timePOC[1], "%d/%m/%Y")), as.numeric(as.Date(timePOM[1], "%d/%m/%Y")), as.numeric(as.Date(timeTSS[1], "%d/%m/%Y")), as.numeric(as.Date(Dates[1], "%d/%m/%Y"))) # starting minimum starting date for forcings and observations
ti=as.numeric(as.Date(Dates[1], "%d/%m/%Y"))-t0 # Start of integration [day]
tf=as.numeric(as.Date(Dates[2], "%d/%m/%Y"))-t0 # End of integration [day]
# Prepare t data for Temperature and Feeding interpolation
timePOCseries=as.numeric(as.Date(timePOC, "%d/%m/%Y"))-t0 # Days at which POC measurements are available
timePOCchseries=as.numeric(as.Date(timePOCch, "%d/%m/%Y"))-t0 # Days at which POC characterization is available
timePOMseries=as.numeric(as.Date(timePOM, "%d/%m/%Y"))-t0 # Days at which POM measurements are available
timeTSSseries=as.numeric(as.Date(timeTSS, "%d/%m/%Y"))-t0 # Days at which TSS measurements are available
# Interpolation of forcings
POCtem=as.vector(matrix(0,nrow=ti-1)) # Initialize vector POCint
CPOCtem=as.vector(matrix(0,nrow=ti-1)) # Initialize vector CPOCint
NPOCtem=as.vector(matrix(0,nrow=ti-1)) # Initialize vector NPOCint
POMtem=as.vector(matrix(0,nrow=ti-1)) # Initialize vector POMint
TSStem=as.vector(matrix(0,nrow=ti-1)) # Initialize vector TSSint
i=ti:tf # Interpolation base points
POCtem2=approx(timePOCseries,POC,xout=i) # POC interpolation according to base points
CPOCtem2=approx(timePOCchseries,CPOC,xout=i) # CPOC interpolation according to base points
NPOCtem2=approx(timePOCchseries,NPOC,xout=i) # NPOC interpolation according to base points
POMtem2=approx(timePOMseries,POM,xout=i) # POM interpolation according to base points
TSStem2=approx(timeTSSseries,TSS,xout=i) # TSS interpolation according to base points
POCint=c(POCtem, POCtem2$y) # Interpolated POC values starting at t0
CPOCint=c(CPOCtem, CPOCtem2$y) # Interpolated CPOC values starting at t0
NPOCint=c(NPOCtem, NPOCtem2$y) # Interpolated NPOC values starting at t0
POMint=c(POMtem, POMtem2$y) # Interpolated POM values starting at t0
TSSint=c(TSStem, TSStem2$y) # Interpolated TSS values starting at t0
# Prepare dates vector
daysPOC <- seq(as.Date(timePOC[1], format = "%d/%m/%Y"), by = "days", length = length(POCint))
daysCPOC <- seq(as.Date(timePOCch[1], format = "%d/%m/%Y"), by = "days", length = length(CPOCint))
daysNPOC <- seq(as.Date(timePOCch[1], format = "%d/%m/%Y"), by = "days", length = length(NPOCint))
daysPOM <- seq(as.Date(timePOM[1], format = "%d/%m/%Y"), by = "days", length = length(POMint))
daysTSS <- seq(as.Date(timeTSS[1], format = "%d/%m/%Y"), by = "days", length = length(TSSint))
# Check if forcings are Ok with integration extremes
if ((ti<(as.numeric(as.Date(timeT[1], "%d/%m/%Y"))-t0))|(ti<(as.numeric(as.Date(timeChla[1], "%d/%m/%Y"))-t0))|(ti<(as.numeric(as.Date(timePOC[1], "%d/%m/%Y"))-t0))|(ti<(as.numeric(as.Date(timePOCch[1], "%d/%m/%Y"))-t0))|(ti<(as.numeric(as.Date(timePOM[1], "%d/%m/%Y"))-t0))|(ti<(as.numeric(as.Date(timeTSS[1], "%d/%m/%Y"))-t0))) {
cat("ERROR: forcings are beginning after the specified integration start\n")
cat("Impossible to proceed with interpolation\n")
}
if ((ti>(as.numeric(as.Date(timeT[2], "%d/%m/%Y"))-t0))|(ti>(as.numeric(as.Date(timeChla[2], "%d/%m/%Y"))-t0))|(ti>(as.numeric(as.Date(timePOC[length(timePOC)], "%d/%m/%Y"))-t0))|(ti>(as.numeric(as.Date(timePOCch[length(timePOCch)], "%d/%m/%Y"))-t0))|(ti>(as.numeric(as.Date(timePOM[length(timePOM)], "%d/%m/%Y"))-t0))|(ti>(as.numeric(as.Date(timeTSS[length(timeTSS)], "%d/%m/%Y"))-t0))) {
cat("ERROR: forcing are ending before the specified integration end\n")
cat("Impossible to proceed with interpolation\n")
}
# Spatialized forcings upload
# read .nc files
sst <- raster::stack(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//sst.nc"))
chl <- raster::stack(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings/chl_a.nc"))
# transform rasters to points
pixel_sst <- t(raster::rasterToPoints(sst))
sst_export <- pixel_sst[-c(1,2),]
#colnames(pixel_sst) <- gsub("V", "sst", colnames(pixel_sst))
write.csv(sst_export,paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//sst.csv"))
sst <- read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//sst.csv"),header = TRUE)
sst <- sst[,-(1)]
colnames(sst) <- gsub("V", "sst", colnames(sst))
pixel_chla <- t(raster::rasterToPoints(chl))
chla_export <- pixel_chla[-c(1,2),]
#colnames(pixel_chla) <- gsub("V", "chl", colnames(pixel_chla))
write.csv(chla_export,paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//chl.csv"))
chl <- read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//chl.csv"),header = TRUE)
chl <- chl[,-(1)]
colnames(chl) <- gsub("V", "chl", colnames(chl))
# save coordinates points
write.csv(pixel_sst[1:2,],paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//coordinates.csv"))
coord <- read.csv(paste0(userpath,"/Mussel_spatial/Inputs/Spatial forcings//coordinates.csv"))
forcings=list(timeT,sst,timeChla,chl,daysPOC,POCint,daysCPOC,CPOCint,daysNPOC,NPOCint,daysPOM,POMint,daysTSS,TSSint,coord)
return(forcings)
}
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